<tool id="ab_index" name="Abundance index" version="0.1">
    <description>computation across species, sites and years</description>
    <requirements>
        <requirement type="package" version="3.4">r</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        Rscript '$__tool_directory__/ab_index.R' '$__tool_directory__/dennis_gam_initial_functions.R' '$input1' '$input2' '$output' ]]>
    </command>
    <inputs>
        <param format="tabular,csv" name="input1" type="data" label="Count file" help="The file must contain the SPECIES, SITE, YEAR, MONTH, DAY and COUNT columns. CSV file separator ',' or tab."/>
        <param format="tabular" name="input2" type="data" label="Flight curve output"/>
    </inputs>
    <outputs>
        <data format="tabular" name="output" from_work_dir="data.index" />
    </outputs>
    <tests>
        <test> <!-- FAILED -->
            <param name="input1" value="gatekeeper_CM"/>
            <param name="input2" value="flight_curve_result.tabular"/>
            <output name="output" value="data_index.tabular"/>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark 

==========================
Compute abundance index
==========================

This tool is an implementation of the abundance_index function from `RegionalGAM package:  https://github.com/RetoSchmucki/regionalGAM/

This function compute the Abundance Index across sites and years from your dataset and the regional flight curve.

    ]]></help>
    <citations>
        <citation type="doi">10.1111/1365-2664.12561</citation>  
    </citations>
</tool>